Storm Warning
by TardisTheory
Summary: The Doctor has his hands full when he and his companions stumble upon tornado damage that isn't quite right. Storm chaser video proves that the tornadoes may have extra-terrestrial ties, and only the Doctor can find out what's really going on!
1. Twister!

Alright, you know the drill. Don't own Doctor Who. Wish I did. But I don't. R&R Please! :D

Also, shout out to Queenofthebadlands. This is the story I told you about!

* * *

_**Storm Warning**_

_Chapter 1:_

_ Twister!_

" You look ridiculous in that." Amy mock scolded as the Doctor fiddled with a cream colored cowboy hat on his head. It didn't match anything he was wearing - not the brown blazer, the pinkish shirt, or black pants and shoes, not to mention the red bow tie. He was standing in front of the main control board of the TARDIS. The components made a soft whirring sound that provided constant background noise.

"I think I look rather dashing." The Doctor said with a smile. He turned and began pushing a few buttons on the console. After a few moments of this, he spoke again. "I'm taking you to the old west."

Amy's eyes lit up. "Well, that explains the hat." She said. She followed the doctor around the console as he flipped a few levers and pressed more buttons. "Why the old west?"

They heard Rory's footsteps on the metal stairs as he climbed to the platform.

"Well, it was Rory's turn to choose." The Doctor smiled at the two. "You picked Venice, now Rory has chosen the old west."

"I didn't choose Venice." Amy said in defense. "That was all you."

"You chose Rio."

"We didn't get to Rio!"

"Oh. Guess you're right. Well then." He said, dodging her comment. He pulled one last lever. The TARDIS began to wheeze, and the whirring of the machines got louder.

Amy and Rory both took a few steps back and grabbed onto the railing around the platform. The TARDIS lurched a few times.

The lights rattled, the floor shook, but nothing seemed to even phase the Doctor. He just kept on making his rounds, checking the instruments as if the whole place was as still as a lake at sunrise.

Rory and Amy were used to this now, but they still held on for safety.

As quickly as it started, it was over. The wheezing came to a stop, and the time machine ceased its shaking. The Doctor bounded past Rory and Amy, down the stairs and over to a pair of white paneled doors (only one of which actually opened). "Welcome to Dodge." He said as he flung the door open.

Rory glanced at Amy. He almost couldn't contain his excitement. He'd loved cowboys as a child, and this was like a dream come true for him. "Come on, Amy!" He grabbed her arm and pulled her after the Doctor.

The air outside was still and hot when the three exited the TARDIS and found themselves face to face with a black cow. She stared blankly back at them. She wasn't concerned that a big blue police box had just materialized in front of her, nor that two humans and a Time Lord had just spilled from its belly. She just stood there, chewing her cud and refusing to move.

"Cows." The Doctor said. The oil industry of the west." He looked around, his faced puzzled. "This isn't right." He looked out over the yellow-and-green-colored hill they had landed on. The grass didn't move at all in the stillness.

"What's not right?" Amy asked as he walked away, still wearing that awful hat.

The Doctor weaved his way through the rest of the cow heard. "The fences. This is the old west. There shouldn't be fences." His hand moved instinctively to the sonic screwdriver in his pocket. "And the landscape isn't quite right..."

Amy took a good look at the fence posts. At first glance, they were all wooden, but as she squinted at them, she saw more modern, metal posts in between the wooden ones. "Doctor..."

"Not now, Amy!" The doctor called across the field.

Rory rolled his eyes. "This isn't the old west. Look. There's a road. A paved road." He said, pointed to his left. A little way down the hill, there was a two lane country road. They all heard a rushing noise that started soft, but became louder and louder. From behind another part of the hill, a convoy of cars appeared, speeding past, bending the large antennas on top in the wind. A few of them also had instruments on the tops that spun as the wind rushed by.

"What is that?" Rory asked.

The Doctor approached them from behind, and stopped. "A bunch of storm chasers by the looks of it." He said.

Amy and Rory whirled around. "You know, the _least_ you could do is warn us when you're going to do that." Rory complained.

"Ah, but where's the fun in that?" The Doctor laughed.

"So where are we?" Amy chimed in, voicing the question that was on all of their minds. Or, at least, her and Rory's minds. By the look on his face, she gathered that the Doctor had already figured it out.

"Not the old west, that's for certain." He answered. A gust of wind blew the ten-gallon hat off his head. "My hat!" He exclaimed. It fell to the ground several yards away, but was quickly scooped up by the wind again.

That was when they noticed the storm clouds towering into the sky. The white cloud-tops boiled upward. The underside of the storm raged in purple and gray fury. The wind gusted again, pulling the grass in the direction of the storm.

"Look at that! Absolutely magnificent!" The Doctor shouted over the noise of the wind, his hat now completely forgotten as it tumbled away over the top of the hill.

"It's a thunderstorm." Amy remarked.

"Not just any thunderstorm." The Doctor explained with a smile. "It's a supercell. The most dangerous of thunderstorms. This is what the storm chasers were after."

Rory remembered the books he'd read on storms back in grade school. He suddenly felt worried. "Well, storm chasers are after tornadoes. If they're chasing this storm, then maybe we should consider getting away."

"Nonsense, Rory!" The Doctor said. He put his arms over the shoulders of both of his companions. "How about our own little chase, hmm? I'd wager neither of you have seen a tornado up close before."

"You're insane." Rory commented and shook the Doctor's arm off. He looked glaringly at Amy, trying to relay the message that she should do the same. "Amy, you agree with me."

"Oh, don't tell me you're afraid of a little thunder." Amy teased. "Come on. The Doctor knows what he's doing."

"So, you're telling me he's a storm chaser, too?" Rory said incredulously. "It takes _years_ of study to storm chase!"

The Doctor smiled and patted the younger man on the back. "Trust me, Rory. I've been around for a while."

"That doesn't mean you know everything." Rory muttered.

The Doctor ignored Rory's comment and led the way back inside the TARDIS.

"Doctor, you still haven't told us where or when we are." Amy pointed out as the Doctor began flipping controls again. She watched him from the lower floor.

"Spring of your time, it looks like." He explained.

"Where are we going?" Rory asked, secretly hoping that the Doctor was recalculating to get to the old west. If just once, they could make it somewhere he said he'd take them...

"Same time. Just into town." The Doctor pointed at the TARDIS screen. "See this map? We're just outside of Norman, Oklahoma. I'll get us into town, get us a a car, and we can go after this little storm."

"What about the TARDIS?" Amy asked.

"I'll hide it." The Doctor replied simply.

"You can hide the TARDIS?"

"It's actually quite easy, though I won't go into the physics of it. It's a bit complicated."

* * *

Amy opened the door of the TARDIS and saw the side of a strip-mall. "What's this?" She asked.

"American consumerism at its best." The Doctor replied as he walked up behind her. Rory followed the Doctor. "It's a strip-mall. There's an auto rental place at the end."

Amy poked her head out and looked around a bit. There was the shopping center, a parking lot, and what appeared to be residential areas around it.

"How did you know that?" Rory asked.

"I installed a GPS in the TARDIS. " The Doctor answered. "Any more questions?"

Amy and Rory stopped talking. Suddenly, they heard blaring sirens. How had they not noticed the bright flashes of lightning or the deafening thunder?

"Tornado sirens!" The Doctor exclaimed, grabbing the door and shutting it in Rory and Amy's faces.

He raced back up to the deck that the console sat on. Hurriedly, he got the TARDIS up and running. Once again, levers and buttons awoke the time rotor.

Rory looked into Amy's amber eyes. "It's going to be okay." He assured her, though he wasn't really all that sure.

The TARDIS wheezed, and shook. The wind howled outside, but began to fade. Before they knew it, the wheezing had stopped. So had the sirens.

"We're an hour in the future." The Doctor explained before Amy and Rory could ask. He opened the TARDIS door. The sun was setting, and the storm's towers could be seen on the eastern horizon. Odd lightning jumped in the clouds, causing soft, distant rumbles of thunder. He turned his attention to the shopping center. It had been completely destroyed. No...destroyed wasn't even the right word for the carnage that lay before them. Not only was the strip-mall completely leveled, but there was a large gash in the earth itself. It snaked through the parking lot, varying between ten and fifteen feet deep. Cars, wood, and building materials were strewn about the entire area, but made much more of a visual impact in the earth's wound. It was like a fault had opened up in the parking lot!

"Quick, out of the TARDIS." The Doctor hissed. As soon as Amy and Rory stepped out, he pressed a button on the key, and the TARDIS disappeared. "See, told you I could hide it."

Rory thought he detected a hint of smug satisfaction in the Doctor's voice, but if he did, it didn't last long. The Doctor was off to the parking lot where camera crews were gathered around the new miniature-sized canyon.

"This isn't normal." Rory whispered.

"I know." The Doctor replied. "I need to check this out."

The first car they came to stood out against the menagerie of news vans. It was a yellow armored SUV. The driver, a man in his late 20's, was standing in front with his camera. He had blonde hair that was cut close to his head, and eyes the color of a clear sky.

The three heard his voice as the camera rolled. "I told them this was happening. No one believed me before now." He was shaking, as if the full scale of what had happened was just now hitting him. "I warned them!"

The Doctor's attention pricked. He approached the man with the camera, leaned into his face, and without any formal introduction, demanded to see his video. "Camera. Now."

"You actually want to see my footage?" The man asked in a voice that carried a trace of a southern drawl. At first he was surprised, but the surprise faded into suspicion. A young man in an outfit better suited for an old college professor was asking to see his videos, and for him, that was very odd.

Amy grabbed the Doctor's arm. "I am so sorry about this." She said as she pulled him out of the man's face, once again astounded at the Doctor's lack of respect for personal space. "He researches...odd happenings."

The Doctor didn't seem pleased with Amy's lie, but he went with it out of necessity. "Yes, we're from a program in London. Heard about your videos and thought there might be something to them."

"Who are you?" He asked.

Amy answered. "Well, I'm Amy, this is Rory, and he is-"

"People just call me the Doctor." He interrupted.

The man looked nervously at the Doctor. "I'm Marshall Welch. I'll show you the videos, but not here. Come with me. I live in town."

The Doctor followed without question. He was keen to figure out what exactly was going on.

Amy and Rory hung back a little. "It's okay." Amy said to Rory. She grabbed his hand and pulled him after the Doctor.

They climbed inside the yellow tank.

"You added extra plating." The Doctor noted.

Marshall nodded. "I'm an extreme storm chaser. My goal is to drive this thing right into a tornado."

Rory and Amy buckled themselves into the back seat of the vehicle. There were wires all around them, all connected to laptops taking readings. Lights flashed and flickered from dark places under the seats and along the cables. "Into a tornado? Are you insane?" Rory asked.

"You have to be if you want to chase at all." Marshall laughed.

"So, besides the large hole in the ground, what is different about these tornadoes?" The Doctor asked.

"Well, that's just it." Marshall explained. "There is not fundamental difference. We got some readings off that last one saying the winds were around a hundred and twenty miles per hour. But the damage is consistent with a powerful EF-Five."

"EF-Five?" Amy whispered.

"Tornado strength scale." Rory whispered back. "Five is as high as it goes."

The Doctor looked pensive. "Anything else?"

"Well, we've noticed an odd glow from the tornadoes."

At this, the Doctor's expression changed to one of extreme worry. "You're right about these being odd tornadoes, but they aren't all natural."

"What do you mean?" Marshall asked.

Amy and Rory already knew what was coming.

The Doctor glanced at Marshall, then at the two in the back seat. He sighed lightly, then revealed the suspicions that had now crystalized into facts in his mind. "You're dealing with extra-terrestrials."


	2. Wing in the Sky

This chapter is a bit shorter than the first. Sorry about that. Expect the next to be longer.

* * *

**Storm Warning**

Chapter 2

_"Wing in the Sky"_

"Aliens?" The word rolled off Marshall's tongue slowly, as if it was completely foreign to him. "Are you crazy?"

"Completely." The Doctor said absentmindedly. He was too busy thinking to notice that Marshall had not said 'serious.' He rubbed hid chin. "But why are they here...?" His voice trailed off.

Marshall pulled the car into the driveway. He grabbed his camera from the back while the three time travelers disembarked from the car. Rory helped Amy out of the back seat. "Here we go again. More aliens."

"Oh shush. You like these adventures." Amy said playfully.

Rory gave her a hard stare. "I like them, but they're not what I want. You know that."

Amy put her arms around him. "I love you, Rory."

"I love you too." He said. "Let's just try to stay safe until this is over."

The Doctor pushed past the two and followed Marshall.

"All I know is that at the start of this chase season, we hadn't ever seen anything like that." The storm chaser said.

All three followed Marshall inside. He led them down a dark hall. The carpets in the house were clean, but looked like they hadn't been replaced since the 1970s. The walls were wood-paneled, and the lighting was sparse.

At the end of the hall, a door was closed and locked. Marshall flipped through the keys on his key chain until he found the right one and unlocked the room.

It was the same as the rest of the house – clean, but outdated. The wallpaper was an ugly stripped pattern, and the two chairs were straight out of a seventies shag pad. The only modern thing in the room was a computer desk and the computer sitting at it. The monitor was a flat screen, and around it and the keyboard were several external hard drives, all blinking with little green and red lights.

"Hold on." Marshall said. He took his camera and plugged it into the tower if the computer. He clicked the mouse a few times, and a window popped up. "Look at this."

Amy, Rory, and the Doctor gathered around the screen.

The video was astounding. It was a black tornado literally cutting through the field. However, it was lit from inside the funnel, giving it an eerie blueish-white glow.

"The tornado is black because of the amount of soil in it." Marshall explained. "We don't know what is causing the glow."

The Doctor sat a plastic chair next to Marshall's office chair. stared at the video, completely entranced by the glowing twister. His eyes spotted something in the clouds. "What's that?" He asked, pointing to a tiny gray spot near the top of the tornado.

Marshall leaned in. "I hadn't noticed that before..."

"It's metal!" Amy exclaimed.

The Doctor smiled. "Exactly. Can you zoom in on that?"

Marshall made a few clicks on the screen, then took the mouse and pulled a green box around the area to be enlarged. When he released the button, the selected area grew to fill the screen, and the storm chaser gasped.

Sticking out from the cloud-base was a wing. Or, more accurately, part of a wing. Foreign symbols marked the object, and proved that it wasn't of Earth. It was floating in one place, very close to where the funnel cloud had descended from.

"Is that..."

The Doctor nodded. "A spaceship? Yes. You didn't see this in the sky?"

Marshall shook his head. "Never noticed it."

"You want to know why you can see it now, and didn't notice it then? Perception filters. Since a camera is not human, and therefore has no brainwaves, it can see right through them! Haha!" He clapped his hands together and jumped to his feet. "But, wouldn't they know this planet is filled with video cameras that can see them?" He started pacing back and forth across the small room.

"Wait a sec. What?" Marshall said in disbelief.

Rory gave him a sympathetic look. "You get used to it. We-"

"Shush! I'm thinking!" The Doctor barked, cutting Rory short. "If these aliens are so unconcerned with discovery, that means one thing. They're desperate."

"So what does that mean?" Amy asked.

"It means we need to get back to the TARDIS." The Doctor answered. He headed toward the door of the room, Amy and Rory not far behind.

"Wait. You're not just going to leave, are you?" Marshall's severely disappointed voice said behind them. He was out of his chair and right behind them. He stopped them at the front door. "You can't just leave me behind. Not after this!"

"No, I can't let you go." The Doctor said. "You don't know the risks. I'm sorry."

"Did you miss the part about how I drive into tornadoes?"

The Doctor sighed, keeping the ever-tight leash on his temper. "What are your credentials?"

"Four years in the University of Oklahoma meteorology department, two more getting a masters in meteorology."

"And no experience with Aliens. Give me your phone." The Doctor said.

Marshall had his phone out almost before the Doctor finished speaking.

"Rory, put your phone number in his phone."

Rory rolled his eyes. "Fine."

As he typed, the Doctor gave Marshall instructions. "Stay here. Keep a low profile. We'll call you if we need you. And...we may need you."

Amy smiled at him. "If you're here, then you can help us if we get into trouble."

Marshall nodded.

The Doctor opened the door and motioned Amy and Rory out. Before he followed them, he took one last look at Marshall. "We're not joking. You may be the only person who can save us if something happens." And with that, he too was out the door.

Marshall looked at the cell phone in his hands. "Wow..." He whispered.

Suddenly, the door opened again. It was Amy. "You wouldn't mind giving us a ride back to the strip-mall, would you?"

* * *

The Doctor handed Rory the TARDIS key. Find the TARDIS, and get it unlocked. I'll be over in a bit."

Amy stayed with the Doctor as Rory strode away. "You told Marshall to stay because you don't like him." She said.

The Doctor looked up. "Of course not. It's just like I said. It's too dangerous for him."

Amy wasn't convinced. "He's older than both me and Rory, and knows more about tornadoes than either of us. Why did you leave him?" Her tone was more demanding this time.

The Doctor sighed. "He's a thrill-seeker. I don't need anyone like that on the TARDIS."

Amy huffed. "Yeah. Already got one of those." She said with a role of her eyes.

The Doctor turned on her, putting his face very close to hers. "I have been around for nine-hundred and seven years. I am NOT a thrill-seeker. Though I do enjoy the dangers we sometimes end up facing, I don't go _looking_ for risky situations." He turned on his heel and went to inspect the damage. He surveyed the long opening in the parking lot. Then, he pulled out his sonic screwdriver and waved it along the edge of the hole. It made a whirring noise, and glowed its characteristic green color.

"What is it?" Amy asked.

He whipped the sonic screwdriver in front of his face. The prongs flashed up, and he checked the reading. "The energy readings on this. There's a residue left here that comes from some energy beams." He chuckled a bit. "I think I know why that tornado was glowing."

"So these aliens are shooting energy beams at the Earth." Amy said. "And using the tornadoes to hide them."

"Yes. Now we just need to find out why." The Doctor said.

"Uh, Doctor?"

Amy and the Doctor turned around. Rory was standing where they had parked the TARDIS. "Doctor. I've walked up and down this whole area, and the TARDIS isn't here."


	3. Night Terrors

Sorry for the lengthy delay. Been SUPER busy lately. But, here's a long chapter to make up for it. Reviews are greatly appreciated!

* * *

_**Storm Warning**_

Chapter 3

_Night Terrors_

"Wait. What?" The Doctor exclaimed. What do you mean it's not here?"

Rory didn't know what to say. "It's just...not here."

The Doctor took his sonic screwdriver and waved it in Rory's direction. Nothing happened.

"What are you doing?" Amy asked.

"Just like the sonic waves disrupt perception filters, they also disrupt the invisibility circuit on the TARDIS. I mean, it's really just a fancy perception filter anyway." He scanned the area again, this time flipping up the four prongs on the top of the screwdriver. "Nothing." He sighed.

"We should call Marshall." Amy said. "We can't just keep standing out here."

The Doctor looked bewildered and frustrated. He snapped at Amy. "We need to find the TARDIS!"

"Doctor, it's not here. You just proved it." Rory said, trying to reason with him.

The Doctor ran his hands through his hair, trying to think. Finally, exasperated and out of options, he agreed with Amy. "Go ahead and call Marshall. We're going to need help."

* * *

Marshall seemed delighted to hear Amy's voice again. He was over with his yellow tank of a truck within minutes. As he pulled up, he rolled down the window. "Heard you were in need of a bit of assistance!" He laughed.

Amy and Rory smiled, but the Doctor kept his face blank. He was lost in thought. Who could have taken the TARDIS? Looking back, leaving it around so many reporters probably was a bad idea, but none of them had been anywhere particularly close to where he had parked it. A darker thought crossed his mind, but he pushed it away. It was too unlikely to be considered.

He opened the door for Rory and Amy, then walked around the car and got in the front seat himself.

"So, what's going on?" Marshall asked as he got the car moving again.

The Doctor looked right at Marshall. He was going to need the truth, now that the TARDIS was missing. "Okay, truth is, we're not from a research program. We're time travelers. And my time machine has gone missing. Without it, getting rid of your alien problem will be tricky. Not impossible, but...very tricky."

Marshall opened his mouth, as if he wanted to say something, but a jumbled mess just came out instead. "Time tra-TIME? _TIME_?" He starred at the Doctor in disbelief. "I had trouble believing your aliens story, but this...this..."

"Hey! Eyes on the road!" Amy scolded.

Marshall sheepishly turned his eyes away.

For a while, there was an oppressive silence in the car. The Doctor was lost in his own world, while Amy and Rory could think of nothing to say. Besides, if they did say anything, he would shut them up quickly. After all, he was thinking. They knew he needed silence to think.

"I need more to go on." The Doctor said finally. "I can't identify these aliens with much certainly without a better look at that ship."

"We'll have to wait for the next storm." Rory pointed out.

"He's right." Marshall agreed. "I haven't heard of them appearing outside of the storms."

"Well, the perception filters would prevent you seeing that." The Doctor mused. "They're probably out hunting storms, just like you." He motioned to Marshall. "The difference is that they can tell exactly which storms will produce tornadoes and which won't."

Marshall's eyes widened. "Seriously? Do you know how many chasers would _kill_ for that technology?"

The Doctor gave him sidelong glance. "Yes. Which is why you absolutely cannot tell any other storm chasers that it exists. Too many wars have started over such petty matters. You humans will get the technology...eventually." His eyes shifted back to the road they were traveling down.

Next thing the three knew, they were back in Marshall's house, readying themselves for bed. The Doctor had allowed Amy and Rory to have the couches, relegating himself to the floor. He shook off his jacket and hung it from the back of the couch Amy was laying on, then began to loosen the bow-tie at his neck, finally managing to get it to the point of hanging limply around his neck. He kicked off his shoes and socks and left them by the sofa as well. Finally, he pulled his suspenders off his shoulders and let them hang at his waist.

"All I have are these blankets and this sleeping bag." Marshall said. "I hope you won't mind."

Amy shook her head. "Of course not. Thank you for being so kind to us."

Marshall could feel his face flushing slightly. "You're welcome, Amy." He replied.

Rory reached across the small gap between the catty corner couches and placed his hand protectively on Amy's shoulder. He could see the problem written all over their host's face, and he didn't like it.

"Well, I guess I'll get to bed." Marshall said, turning to leave. "Night!" He closed the door to his room across from the living room quietly.

The Doctor waited until after he had gone to speak. "So, what do we make of this?" He whispered.

"Well, we're stuck in America with no TARDIS and aliens are attacking the city we're staying in." Rory whispered back, a hint of frustrated sarcasm in his voice. "Just another day in the life of the Doctor."

"Rory!" Amy hissed.

"What? I said we should get back in the TARDIS and go to the old west. _You_ wanted to chase tornadoes with the Doctor."

The Doctor interceded. "This isn't the time for bickering. Now, what's done is done. Get some rest, and we will see what happens in the morning." He turned over under the blanket Marshall had given him and closed his eyes. His mind however, keep moving. Always moving. He had once told Amy that he thought so much that it became hard to keep up. Now was no exception. He felt like he was so close to identifying these aliens. _"But something's missing..."_ He thought to himself. Finally he drifted off to sleep, lulled by the sound of Amy's barely audible snoring.

* * *

CRASH!

The Doctor sprang awake, kicking at the blanket and flailing his arms. He sat upright and looked around the room. Rory and Amy seemed to have missed the noise and still slept. Lightning flashed in the windows again, followed by another loud crack.

Down the hall, a light was on and glowed under the door of Marshall's office. The Doctor pulled himself to his feet and walked toward the door. His barefoot feet hardly made any noise as he approached. He could hear the rain pelting the roof, interspersed with thacks and thunks from hail. He knocked on the study door. "Marshall?" He asked. "Some storm. Mind if I join you?"

For a few seconds, there was no answer. Then, Marshall opened the door a bit. "Doctor." He said, and opened it further. His face looked very worried. "Actually, this is perfect. Something's really wrong with this storm."

The Doctor felt his mind beginning to whirr again now that the shock of being awaken so suddenly was wearing off. He followed the man in, ignoring his lack of a shirt.

Marshall sat down at his computer and pulled up a radar look at the storm over Norman. At first glance, nothing seemed wrong with the storm. The Doctor didn't notice anything amiss.

"It looks normal here." Marshall said, "but when you look at the wind, moisture, and lack of triggers, this storm is really strange. According to all of the readings in the area, it shouldn't exist at all, and it really shouldn't be this strong!"

"No. It shouldn't..." The Doctor said in a low tone. His toes picked up on something. "Do you feel that?" He asked.

"Feel what?" Marshall replied.

"The vibration." The Doctor said ominously.

The vibration got stronger and stronger until it wasn't just the Time Lord feeling it. The whole house was rattling!

In the background, tornado sirens screeched to life, wailing in the darkness.

"Doctor!" Amy shouted from the living room.

The sounds were becoming deafening. The Doctor and Marshall both looked up as the power flickered out.

"Doctor! What's going on?" Rory yelled.

"Quick, everyone to the basement!" Marshall commanded.

Amy and Rory rushed into the hallway. Amy shoved the Doctor's coat, shoes, and socks into his arms. "Here!" She had somehow already managed to get her converse back on.

Marshall pried open a door that, just moments before, had just been part of the wall. The stairwell descended into complete darkness.

"I'll go first." The doctor said. He pulled out his sonic screwdriver and bathed the stairs in green light. Marshall let Amy and Rory go next. Then he stepped onto the first stair, closing the door behind him.

The basement didn't do much to stifle the vibrations in the earth, but it did cut down on the noises from the weather enough that they didn't have to shout at each other.

"I have a flashlight down here somewhere." Marshall muttered. The Doctor pointed the screwdriver around the edges of the room, lighting up metal shelves strewn with tools. The light spilled onto a desk, and Marshall made a grab for two black flashlights on the top. He kept a larger metal one for himself, and handed a smaller, rubber coated one to Amy.

"Doctor, what's happening?" Amy asked, her voice quivering with terror. Rory had his arms around her, trying to be her protector. Unfortunately, he looked more unsure than she did.

"Something must have created the storm." The Doctor said.

"Yeah." Marshall agreed. "There was nothing natural about that storm. It must be the aliens!"

"Well, you seem to have warmed up to this whole 'time travelers and aliens' thing." Amy jabbed.

Marshall laughed softly. "Guess so."

"Ohhhhhh, how could I not realize this!" The Doctor interjected. "The aliens. It's the Jexian!"

"The who?" Rory asked.

"The Jexian. One of the only races known to have created the technology to create and manipulate weather patterns. But this doesn't make sense, why are they destroying the Earth. They're normally a peaceful race! And they're so far from home. It doesn't make any sense."

"Well, that explains how they could hover basically _in _the tornado." Marshall said. "Their ships are designed for it."

Suddenly, the shaking became even more violent. Things began falling from the metal shelves. Amy, Rory, and the Doctor huddled together in the center of the room, while Marshall paced around them.

They could hear glass shattering above them. The wood of the house creaked. It was never meant to withstand something as powerful as this!

A terrible and loud ripping sound was heard, and part of the basement roof was gone, letting in the screaming wind.

"Everybody hang on!" The Doctor shouted. He put his arms protectively around Amy and Rory and pushed them flat to the ground. Marshall made a dive into the tornado position, his head between his legs, and his hands covering his neck.

Amy screamed as debris pelted them all, causing painful scratches and bruises. "Doctor!" She screamed. It almost felt like the wind was picking them up. It was certainly moving them. One of the shelves crashed to the floor.

"Keep your heads down!" The Doctor yelled again. All of them were now flat on the floor, trying to stay out of the way of the metal missiles flying around them. He stuck his hand into his pocket, making sure to keep a good hold on his trusty screwdriver.

Nothing could have prepared them for this. The howling wind, the almost constant lightning, the terrifying thunder claps, the rumbling earth... Everything was chaos. And at this moment, even the Doctor was afraid they might all perish.


	4. Devastation

Got a few comments about the last chapter being too serious, so I made sure this one felt more like Doctor Who. :) Reviews are always appreciated!

* * *

**Storm Warning**

Chapter 4

_Devastation_

And just like that, it was all over. The wind faded away, and the earth ceased its trembling. For a few moments, none of them moved.

The Doctor raised his head and looked around the black room. He leaped up off Rory and Amy and grabbed his screwdriver again for light. "Marshall!" He yelled.

The younger man's coughs broke through the silence. "Over here." He said, shifting a pile of wood off of himself.

Amy clicked her flashlight on and shined it in the man's face."

"Are you hurt?" Rory asked, finally felling like he could really be helpful.

"A few scratches. I'll be fine." Marshall said, hauling himself to his feet. He raced up the stairs to the door.

He tried to open the it, but found it completely stuck. He threw his weight against it, slamming himself repeatedly against the wood.

The Doctor watched the rather pathetic scene for a moment, then turned and surveyed the room. He smiled as an idea crossed his mind.

"We're trapped." Marshall reported from the top of the flight of stairs.

"No we're not!" Came the Doctor's voice in a happy, almost sing-song tone. "Rory, help me lift this shelf thing."

"What's he doing?" Amy asked Marshall.

The Doctor explained before Marshall could open his mouth. "We have two options. Try to build steps to the hole in the ceiling using these shelves, or if that doesn't work, use the shelf as a battering ram and try to get that door at the top of the staircase open."

"Why don't we try the battering ram first." Marshall suggested.

"There's probably something holding the door shut on the other side." Amy said.

The Doctor and Rory pulled the shelf upright. The Doctor then got behind the wooden desk and pushed it toward the hole in the ceiling. It was in the far corner on the right from the staircase. He looked up through the hole and saw the sky. It was clear now that the aliens causing the storm had moved on, taking their weather creating technology with them. Pale moonlight pushed past two beams lying across each other on top of the opening, leaving faint splashes of light and dark on the floor. Rainwater dripped over the edges and formed a pool on the floor. The Doctor saw his reflection in it, and noticed a small trickle of blood running from somewhere beyond his hairline. He snapped back to attention. "Okay. Rory, Marshall, lift this shelf onto the table. Amy, find as many screws as you can."

Marshall and Rory picked up the shelf and hoisted it onto the table. The top shelf was even with the hole.

Amy roamed around the room, shinning her flashlight on the floor, and picking up every small glittering object she could find. With a handful, she returned to the Doctor. "He's what I found." She said, letting the screws of all different sizes roll out of her hand and into his.

"Perfect." The Doctor said with a smile.

He turned and almost jumped on the desk. "I'm going to secure this thing to the wall using these." He got to work with his screwdriver.

"I'm impressed." Amy commented.

The Doctor turned his head as far toward her as he could. "With what?"

"You're actually using that as a screwdriver!"

"Oh, yes." The Doctor laughed. He turned back to the shelf.

"Wait, so that's a screwdriver?" Marshall asked.

"Sonic technology." The Doctor explained without stopping. He crouched down and screwed some screws into the bottom of the shelving unit. "Alright. That _should_ do it. Can't promise anything, thought. Some of those screws were smaller than I would have liked."

"I'll go first." Marshall offered.

"No, no. I'll go. Don't know what we'll find when we get up there." He jumped off the table, grabbed his shoes and socks and quickly pulled them on. Then, he tied his bow tie, slipped on his jacket, stuffed his sonic screwdriver into his pocket, and smiled at Rory. "Can't face aliens without the proper attire, right?"'

Rory rolled his eyes, but smiled. Typical Doctor.

The Doctor climbed back up on the desk, then place a foot tentatively on the first shelf. He grabbed a hold of the metal beams on the edges and began pulling himself up.

"Be careful." Amy said.

The Doctor smiled, but didn't answer. He took another step up; then another, then another. Finally, he found himself even with the edge of the hole in the house's foundation. "Oh no..." He whispered. He scrambled to pull himself on top of the last shelf. Finally, after a few moments he was able to get to his feet.

What he saw was complete devastation. Marshall's house lay in ruins, as did most of the other houses in the neighborhood. "I think you better get up here." The Doctor called down while still surveying the damage. "This is very not good." A long chasm much wider and deeper than the one at the shopping center marred the landscape like a terrible wound. Play sets, swings, cars, fences, and house debris had been thrown haphazardly into the opening. He heard emergency sirens in the distance, steadily growing louder.

Others were beginning to emerge from the wreckage. Across the street, a mother carried her baby out of a storm shelter. Someone else was calling another person's name. A faint reply was coming from a small pile of boards.

Marshall joined the Doctor, a look of pure horror on his face. "This is terrible! No one had any warning!"

As soon as the other neighbors noticed him, they flocked to Marshall. He walked forward to talk to them while the Doctor held back.

Amy and Rory shared the same shocked look as they finally climbed out of Marshall's basement. Rory didn't think twice before joining Marshall. The Doctor and Amy could hear his concerned voice addressing the other residents. "I'm a nurse. Is anyone hurt?"

Amy smiled and felt proud of her fiance.

The Doctor made his way to the edge of the new rift and looked over the edge. The emergency vehicles had finally arrived, but he ignored them. Buried halfway in the ground, a metal object glimmered in the flashing red, white, and blue lights. "Nooooo..." He whispered in disbelief. He flashed around. "Amy, I think we're dealing with more than just the Jexians here."

* * *

Rory, and Marshall helped the EMTs get last of the seriously injured into ambulances. As the cars drove away, the Doctor approached Marshall. "I need to speak with someone who has access to long distance radio. Do you know anyone?" He asked matter-of-factly.

"A radio?" Marshall said in confusion. "Why?"

"I found something in that hole, and it could be the reason all of this is going on. I need to speak with the Jexians. I'm hoping this is one big coincidence, but I'm afraid that it very well isn't."

"I have a friend who works for the National weather service." Marshall said. "We could talk to her."

"Fantastic!" The Doctor exclaimed. "How soon can you speak to her?"

"Uh, Doctor, it's four in the morning. She won't like being woken up so early." Marshall protested, his face flushed, and he was glad for the cover of darkness.

The Doctor wasn't fooled. "Ah, a lady friend?" He said with a knowing look. "Tell you what, I'll take the blame. No need in getting her cross with you!"

Amy smiled. She noticed a tiny light circling her leg. "_A glow fly!_" She thought. But this insect didn't blink. It was a constant light, followed by a long, blue tail. Suddenly, there were two, then Ten, they just kept multiplying! It was then that she realized these weren't bugs...

"Doctor!" Amy yelped. "What is this?"

The Doctor whirled around from his conversation with Rory and Marshall. "Amy!" He yelled. "Amy, you have to move. Do something. Anything. Take a step."

"I can't." Amy whispered. "I can hardly even speak,"

The lights swirled around her, faster and faster.

"Amyyyyy!" The Doctor and Rory shouted in unison.

She began to fade away. "Do something!" She commanded. But it was too late. The lights faded away, leaving the area dark, and eerily quiet.

"Amy!" The Doctor yelled again.

Rory looked completely dumbfounded. "Amy..."

The Doctor knew Rory would be distraught. "Rory. We'll get her back, I promise. I haven't let you down yet, have I?"

Rory said nothing. It was clear he was still shocked that Amy had just vanished. "What happened to her?" He finally managed to croak.

"That was some sort of teleporter. I don't know why she couldn't move, though." He side-stepped Rory and stood in front of Marshall. "We need your lady friend's help. Now. Amy's safety depends on it."

Marshall nodded. He pulled out a small black flip phone and dialed a number. "Jessie? I'm so sorry to wake you..."

The Doctor frowned at the sky. "Where are you...?" He whispered. The sky stayed clear and silent, and the Doctor sighed.

Marshall closed the phone. "Okay, she's on her way over."

The Doctor nodded.

Five minutes later, Jessie Harper stepped out of a black pick up that was outfitted with a tall antenna and lights on the top. She was a formable woman. She had the look of a tough plains girl. Her dark hair was pulled back in a hasty low ponytail. She was definitely pretty, and had an air of intelligence around her. "Oh my God, Marshall! Glad you're okay!"

She looked in disbelief at the large rift. "Marshall...is this...?"

"Yes." Marshall said. "The tornadoes I've been studying did this."

"Wow, I thought you were just making it up...but..." Her voice trailed off.

Marshall blushed, and looked away for a second. Then, he regained his composure. "This is the Doctor and his friend Rory." He explained. "Aliens are causing these tornadoes, and the Doctor needs to use the equipment at the office to contact them."

Jessie laughed. "I think you may have been hit in the head really hard or something." Jessie said.

The Doctor spoke up. "No, he hasn't. It's all true. I need to speak with these aliens. They have our friend, and there's more going on here than I thought. Please, trust me when I say that it is absolutely imperative that we speak to the Jexian."

Jessie didn't know what to say. But, the proof that something very strange was going on was all over the neighborhood. She couldn't ignore it. "Alright, everyone in the truck." She said.

The Doctor let Marshall have the front this time, on account of his obvious feelings for the woman. Rory felt a sense of relief when he realized that the man liked this woman much more than Amy.

"So, they just call you the Doctor?" She asked, a hint of an Alabama twang in her voice.

"Yes, just the Doctor." He replied.

"Well, Doctor. I sure hope you aren't crazy. And I hope I can help in any way that I can if this is all true."

Rory glanced out the window. He could hardly keep himself calm. "_Please be okay, Amy._" He thought. "_T__he Doctor will bring you back. Just hang on._"


	5. The Jexian

I guess you guys noticed that I changed my pen name. I am now "Don't Diss The Sonic." Figured that was a fun name. Also, so excited about "The Pandorica Opens" on Saturday! Anywho, here's chapter 5! Sorry I'm so slow. And this won't go on much longer. It's only planned to be 8 chapters, so we're already half-way there!

* * *

_**Storm Warning**_

Chapter 5

_The Jexian_

Jessie used her key to unlock the back door to the National Weather Service building. "Come on. Let's get this done before most of the people show up and wonder what's going on."

Rory didn't understand what she meant by 'most of the people" not being there yet. It seemed like the place was fully staffed – at four in the morning!

"It's because of the storm." Marshall explained.

The corridors still had a new look to them. The tile was still a sparkling white, and the walls a dull gray. They passed door after door, turned down hall after hall. Finally, Jessie opened a door that led into a small room with flashing equipment. "Okay, we have ten minutes."

The Doctor filed in behind her and Marshall. He pulled out his sonic screwdriver and waved it around the room. He flipped up the prongs and looked at the reading. "Whatever we do here will be recorded." He reported. "I don't think you want that."

Jessie pulled a few cords out of place here an there. "Like I said. You have ten minutes before someone realizes this stuff is unplugged. Now hurry!"

The Doctor sat down in the chair and scooted up to the desk. He put on a pair of headphones and flipped a few switches on two boxes on the desk. He turned a few knobs, then soniced both boxes with his screwdriver. A crackling sound filled the headphones. Once he was sure it was working, he unplugged the headphones and let the sound play through two small speakers on the desk. He leaned back in the chair and put his feet up on the table, swiveling back and fourth slightly as he spoke. " Jexian ship I presume?" His voice was full of the typical overconfidence he always exuded.

A few seconds passed, then a feminine voice replied. "This is an earthbound communication! How did you know we were here?" She didn't sound angry, but more afraid. "Who is this?"

"You should know who this is. You took my friend. You obviously had a reason for it." The Doctor said calmly.

"We do as we are told." The female's voice replied.

"Where's Amy!" Rory blurted out.

"The girl?" She replied. "She's fine."

"Prove it!" Rory demanded.

The Doctor sent a warning glance at Rory and held his finger to his lips, making a very quiet shushing noise. He turned back to the microphone. "Yes, where is our friend?"

There was a long pause, then a new speaker. "Doctor?" Amy's panicked voice came over the radio. "Doctor! Rory! I'm okay! Please save me!"

"Stay calm, Amy." The Doctor said. He addressed the Jexian on the other end. "Alright, Amy is safe. Now, what are you doing destroying the Earth? You've destroyed the homes and businesses of quite a few humans, and I'd say that's out of line, especially for a peaceful species like yourself."

"This conversation is over unless you state your name and how you were able to contact us." The woman said.

The Doctor sighed. If they had been told to take Amy, why didn't they know who he was? "The Doctor, and I used sonic technology to amp up a radio signal." He said in exasperation.

There was an incredibly long pause.

"Miss?" The Doctor prompted.

"So, you are the Doctor. The owner of the TARDIS." She said.

"Yes." The Doctor replied. "Now, how can I get my friend back?"

"An exchange. You for the girl."

"I'm afraid I can't do that." The Doctor said evenly.

"Then you will not get the girl, or your TARDIS back."

The Doctor realized that his initial hunch about the whereabouts of the TARDIS, however inconceivable, had been right. "If you knew about my TARDIS, how did you not know who I am?" He began to ramble. "You're acting on the orders of someone else, and you have never seen me before, but you knew, no, were TOLD to go after my TARDIS. Plus, your voice, you sound scared. You're not from a violent race. Someone's forcing you to do this. Forcing you to kidnap my friends and steal my TARDIS!" He paused. "Tell me, why are you here?"

"That is something I cannot reveal." The female answered.

The Doctor's expression changed to one of understanding. He half-smiled. "Oh, but I already know why you're here."

"Doctor, time's up!" Jessie whispered.

"What?" The Jexian said in shock.

"Meet me tonight, in the field behind the neighborhood you just destroyed. We can talk then." The Doctor said, then clicked the radio off.

Jessie slipped the cords back into their respective connections, then flashed around to the group. "Let's get outta here!" She hissed.

They followed Jessie back out the door and through the halls.

Rory looked incredibly worried. "Do you really know why the Jexians are here?"

The Doctor stopped. He shifted his eyes back and forth twice before looking right at Rory. "I... have an idea."

Rory sighed. "An idea might not be good enough this time, Doctor. We need to get Amy back, and I don't see that happening unless you have a plan."

The Doctor smiled. "Of course I have a plan, Rory!" He patted the other man on the shoulder.

Rory wasn't reassured, but he said nothing. He followed the Doctor and the two meteorologists back outside the building. They crossed the parking lot and arrived back at Jessie's black truck. "You can come back to my place and sleep if you're tired." She offered.

The Doctor thanked her, but declined. "There's something in that hole I need to look at."

* * *

The Jexians were a strange race, similar to humans, and yet so very different. They had long, willowy bodies and limbs. Their skin varied in color from lavender to a gray-blue. The tops of their arms and palms were gray blue, and faded to lavender on the bottom side. Their faces were lavender around the center of the face, and faded to gray-blue on the edges. There were three silver dots on their foreheads, one directly above the nose, and one to each side of the center dot. Their faces were long, with small noses, narrow lips, and large, slanted, sky blue eyes. Amy observed that there were two different colors of hair among the Jexians – dark purple and dark blue. The styles of hair varied as much as human hair styles. Most of the ship occupants were dressed in white lab coats, though she had seen a few in what appeared to be formal robes.

Amy resisted the spindly hands that shoved her back in the small cell. "Take your hands off me!" She commanded as she fought. It was truly a cell. Four walls made of metal bars surrounded her. There were other cells here, too, but all were empty.

The ship itself had shocked her. There were no walls, or at least, walls that blocked the view. Everything was see-through except the floors. It was a giant yellow ball suspended between two large wings. There were two layers to the ball, both made of some sort of clear material similar to glass, but more heat resistant. The outer covering, which was yellow and served as a protective layer, was static, and attached to the wings. The inner layer, however, was clear, and rotated inside the first layer, allowing the decks of the ship to remain flat at all times, minimizing the effects of flight.

"Well, that explains how the ship survives the storms." Amy muttered.

She could see all that was happening on that particular deck. Towards the front of the ship, several of the Jexians were talking and gesturing to what appeared to be a row of scanners and instruments. They looked frightened, and seemed to be arguing about something.

One of the Jexian walked by her cell.

"What's going on?" Amy asked.

He turned around, and looked at her with a strange look on his face. "You speak our language?"

"As far as I know, the only language I speak is English, so apparently, your language is English, too." Amy huffed, a note of pride in her voice.

"No, we do not speak English." He explained. "Our language is unknown to the Humans."

"Whatever. Just tell me what's going on."

The alien sighed. "Well, you're in a prison cell with no communication." He looked around warily. "But it will have to be quick. If they find out one of us has revealed their plan, they'll kill us all. No mercy, that lot."

* * *

The Doctor slid down into the rift, trying and failing to keep himself out of the damp earth. "Right then!" He called. "Rory, you next. I'm going to need a bit of help down here."

Rory, afraid of losing his grip, made his way down the muddy slant gingerly.

"What about us?" Marshall called from the edge.

"Stay up there, keep an eye out for any saucer shaped ships." The Doctor instructed, and then smiled. "Saucer shaped ships. Try saying _that_ four times fast." He turned and began to clamber over piles of wood, twisted metal, and rubble. "The Jexian are here because someone is forcing them to be here." He explained to Rory. "And if what I saw in this..." he gestured wildly around at the hole they were in. "...thing... then we're in a lot more trouble than I first thought." His voice dropped to just above a whisper.

"What kind of trouble is that?" Rory asked.

The Doctor stopped an knelt beside a piece of ply-wood. He lifted it. Underneath it was a glittering silver object. It was egg-shaped, and covered in rows of spots. "The Daleks are forcing the Jexian to do their dirty work." The Doctor hissed. "This is a progenitor. Supposedly, only one survived, and the Daleks got that one, but another one must have landed here on Earth. With this, my greatest enemies can reproduce twice as fast. They're already hard enough to deal with, we don't need more of them out there."

"The Daleks? Daleks like what Amy told me about?" Rory asked in astonishment.

"Yes." The Doctor said. "Now, help me get this piece of wood off of it."

Rory grabbed the plywood while the Doctor picked up the progenitor. "This is why the Jexians knew to take my TARDIS and Amy. The Daleks got smart this time." He didn't mention that if he hadn't seen the progenitor earlier, he still wouldn't know the Daleks were involved. "But why the Jexian? Why not do it themselves?" The Doctor muttered to himself. "Everyone knows the Jexian are a peaceful race. Why them?"

"Maybe the Daleks knew you'd come sniffing around." Rory suggested.

The Doctor looked as if a lightbulb had gone off in his head. "You know, you may be right."

"You have that meeting tonight. We can ask then."

"Not sure I'll get much information that way." The Doctor admitted.

"Why not?" Rory asked.

"They were afraid to speak to me over the radio. Afraid to tell me what they are doing here. The Daleks are monitoring their communications. There might even be a few on the ship. Who knows?" He held up the progenitor. "But, as long as we have this, we've got what they want. This is how we'll save Amy without an exchange for me." The Doctor said with a smile. He put the progenitor in his pocket and proceeded to begin to climb back out of the trench.

Marshall grabbed his hand and pulled him up over the edge when he reached the top. The Doctor dusted himself off as best he could. Rory did the same once he was on top.

"Now then." The Doctor said. "We wait for the Jexian."


End file.
